Understanding the computations that take place in brain circuits requires identifying how neurons in those circuits are connected to each other. In recent years several new approaches (most notably, serial electron microscopy, replication-deficient rabies viruses, and GRASP) have been designed to identify the wiring diagrams of brain circuits. To overcome some of the limitations of the currently available strategies we propose to generate a new genetically-encoded system to trace brain circuits by transsynaptic control of transcription that will open new opportunities for investigating the relationship betwee circuit connectivity and function. The system that we propose is based on the molecular logic of the Notch receptor. In this system, neurons expressing an artificial ligand (sender neurons) activate a genetically-modified Notch receptor on their synaptic partners (receiver neurons). Upon ligand-receptor interaction in synaptic sites, the engineered receptor is cleaved in its transmembrane domain and releases a protein fragment that regulates transcription in the synaptic partners. Our initial experiments in vitro have confirmed the feasibility of this strategy and we propose to apply this design towards identifying wiring diagrams of neuronal circuits in transgenic animals, both in mice and drosophila.